Tracy Bank was concerned. A geochemist, she makes her living studying how water interacts with rocks. And four years ago, when she arrived at the State University of New York at Buffalo, water was definitely interacting with rocks.

Buffalo is perched on the edge of the largest known reservoir of natural gas in America, a geologic formation known as the Marcellus Shale (pdf). The 95,000-square-mile slab, which lies under sizable portions of West Virginia, New York, Ohio, and Pennsylvania, could contain up to 500 trillion cubic feet of natural gas—enough to meet the nation’s natural gas needs for at least two years. Owing to this bounty, the areas above the shale are now in the grip of an unprecedented gas-drilling boom. The gas is extracted using a method called hydraulic fracturing, or fracking, a technique that involves pumping millions of gallons of water laced with chemicals deep underground to blast open the shale and release the gas trapped inside. The blasting is what got Bank worried.

Fracking has already drawn considerable scrutiny from environmental groups, unhappy homeowners, and teams of lawyers who blame the drilling method for polluting pristine rivers, turning bucolic farmlands into noisy industrial zones, and leaking enough methane to make ordinary tap water as flammable as lighter fluid. Bank is now bringing attention to yet another problem: radiation. Her research shows that high-pressure fluids striking the shale could dislodge naturally occurring radioactive compounds such as uranium and strontium, putting groundwater at risk of contamination.

“Shale is a garbage-bucket rock,” she says. “The more organically rich the shale is, the more natural gas is present, but the more other stuff is in there too.”

To determine how fracking fluids mobilize metals in the shale, Bank and her team solicited rock samples from drill sites in western New York and Pennsylvania. When the researchers subjected their samples to beamed ions—a high-precision way to dislodge surface chemicals—they confirmed that shale rocks contain a suite of toxic metals, including uranium, barium, chromium, zinc, and arsenic. Bank also discovered something new and disturbing: The metals were chemically bound to hydrocarbons, the organic compounds that make up natural gas. Separated from the rock, uranium or any other toxic metal could easily hitch a ride when the drilling wastewater is siphoned back to the surface, Bank found.

“If the goal of fracking is to extract that organic matter—the natural gas—then you’re mobilizing the uranium as well,” she says. As a result, she believes, the current methods for cleaning wastewater generated by fracking are woefully inadequate. Right now, water is injected into disposal wells, dumped into evaporation pits, or run through drinking-water treatment facilities. “This water needs to be treated like industrial waste,” Bank says. Otherwise, radioactive material and a slew of other toxic compounds could leach into the groundwater, potentially tainting it for generations.

On the other hand, the arguments for drilling into the Marcellus Shale are hard to ignore. Natural gas is by far the cleanest-burning fossil fuel, producing about half as much carbon dioxide as the energy-equivalent amount of coal. It also contains almost none of the heavy metals that frequently accompany coal. Moreover, our domestic reserves of natural gas are plentiful: The newly tapped deposits in the Marcellus Shale have helped to more than double the nation’s estimated shale gas reserves, from 23 trillion cubic feet in 2007 to some 60 trillion cubic feet in 2009.

The Department of Energy estimates that natural gas produces slightly more than one-fifth of all the electricity used in the United States, and that number is steadily rising. If production continues as planned, over the next couple of decades natural gas could supplant coal as the leading domestic fossil fuel, serving as a cleaner way to heat our homes and fire our electric plants. “We’ve got terrific natural gas resources,” says David Burnett, director of technology at the Global Petroleum Research Institute at Texas A&M University. “Our country is going broke, but the public refuses to realize how much money they’re spending on imported energy.”

Ernest Moniz, director of the MIT Energy Initiative and a former undersecretary of energy, sees natural gas as the energy source of choice until renewable sources like wind, solar, and geothermal become more commercially viable. “Natural gas truly is a bridge to a low-carbon future and could enable very substantial reductions in carbon emissions—as much as 50 percent by 2050,” he says.

Assuming we can tolerate the collateral damage.

Created nearly 400 million years ago on the surface of a shallow inland sea, the Marcellus Shale formed as tectonic plates pushed up the landmasses that created the Appalachian and Catskill mountain ranges and buried the ancient sea under a layer of rock almost two miles thick. This compression process produced gaseous hydrocarbons that expanded and formed pockets and fissures in the rock— formations that now hold natural gas.

For six decades gas outfitters have been devising increasingly elaborate ways to tap those buried reservoirs. In the late 1940s, the Halliburton Corp. of Houston pioneered the use of hydraulic fracturing to squeeze gas and oil from vertical wells in sandstone thousands of feet below the surface. Their technique involved pumping large quantities of water combined with fine sand and chemical additives into the ground. Through a bit of geologic alchemy, the injection shattered rock like a baseball hitting a windowpane, pushing natural gas and oil out of the rock and into the pipe when the water was pumped back out.

However, the technique proved difficult to use in shale deposits, which form in layers that are wide but shallow. Vertical drilling in shale hit too little surface area to suck up enough gas to make the effort worthwhile. “If you can’t turn the well so it goes along the shale formation and a lot of the well is exposed to the gas, you can’t get the gas out economically,” says Anthony Ingraffea, a hydraulic fracturing expert and professor of civil and environmental engineering at Cornell University.

In the 1990s, new drilling technology developed in Texas made recovering gas from shale far more efficient. The big innovation was a motor attached to the drill bit that allowed it to turn 90 degrees and bore horizontally for up to two miles. Boring parallel to the horizontal shale layers exposes much more of the gas deposits. Companies can also drill multiple wells in any direction from just one drilling pad, creating a honeycomb of tunnels miles beneath the surface that can siphon gas from hundreds of acres.

Next comes the even more difficult part. Typi­cally, each well requires 2 million to 10 million gallons of water to extract the gas. As with conventional drilling, the water is mixed with sand to keep the fissures propped open, and with a cocktail of friction-reducing lubricants to make the water slick enough to slide through the pipes swiftly. Machinery has to pump the water at pressures high enough to send it anywhere from 3,000 feet to a mile down. It is not uncommon during drilling for a site to have at least 10 trucks with 1,000-horsepower pumps and for dozens of tanker trucks to make 800 to 1,200 trips transporting water if there is no on-site source.

Despite concerns that fracking could seriously deplete or contaminate local water supplies, in 2010 Pennsylvania issued more than 3,300 natural gas permits in the Marcellus Shale. Almost 1,500 wells were drilled, and thousands more are on the way. Other parts of the country with shale beds (“plays” in industry parlance), such as Wyoming, Colorado, Arkansas, and Louisiana, have experienced similar gas drilling booms.

To comprehend the long-term implications of hydraulic fracturing, you need to visit the region where gas drilling first boomed. It sits above the Barnett Shale, a formation that underlies 5,000 square miles surrounding Fort Worth, Texas. Large-scale fracking began here in 2002. There are now about 14,000 gas wells in the area, and it is there that the environmental fallout of fracking has been most pronounced. Residents have complained for years of contaminated water, poor air quality, and unexplained health problems such as headaches, dizziness, blackouts, and muscle contractions.

Drilling operations have turned some of Texas’s most affluent communities into industrial wastelands. In towns like Argyle and Bartonville, where drill rigs have been erected within a mile of schools, children complain of nosebleeds, dizziness, and nausea. Parents worry about the release of the cancer-causing chemical benzene in the air above gas fields from processing plants and equipment.

Fracking in the Marcellus Shale has not been going on as long as it has in Texas, but residents have already begun to experience its dark side. Just ask Craig and Julie Sautner. When the cable technician and his wife moved to Dimock, an agricultural community of about 1,500 nestled in the rolling hills of northeastern Pennsylvania, they had no inkling they were sitting on top of a mother lode of natural gas—that is, not until an agent from Cabot Oil & Gas, a Houston-based natural gas producer, knocked on their door in May 2008. He offered them $10,000 to lease the mineral rights on their four acres, with the promise of even more in royalties if Cabot struck pay dirt. “You might as well sign it because all your neighbors are,” the man said, according to Craig. “If you don’t, you’ll miss out.”

In August 2008, the company started drilling less than 1,000 feet from the Sautners’ water well. By mid-September the family’s tap water was undrinkable. “I noticed the toilet water was murky, and when I used the water in the sink in the kitchen, it was brown,” Craig recalls. He called Cabot Oil & Gas to complain, but representatives insisted there was no way that Cabot’s drilling process could have contaminated the Sautners’ well water. The gas deposits sit thousands of feet below water wells, the company told him. What’s more, the boreholes that channel the natural gas up to the surface are encased in steel and cement. But without admitting fault, Cabot installed a water filtration system in the Saut­ners’ basement, which now looks like “a science lab,” Craig says.

Tests conducted soon after by the Pennsylvania Department of Environmental Protection revealed that the Sautners’ water contained high levels of methane, the main component of natural gas. Although methane is not normally harmful to drink in concentrations below 10 milligrams per liter, it can evaporate from the water. If it collects in enclosed spaces like basements, it can become flammable and explode or suffocate those who inhale it. The Saut­ners, who have joined with a group of neighbors and filed a lawsuit against Cabot, worry that the methane could explode at any time. “My son asks every night,” Craig says, with no small measure of gallows humor, “ ‘Do you think we’ll wake up in the morning?’ ”

Industry experts respond that it is impossible for their wells to be creating all the environmental havoc their critics charge. “If you calculate the environmental footprint of one drilling operation, it’s smaller than a big-box store,” Texas A&M’s Burnett says. “Most companies employ the same safety practices they use with industrial petrochemical facilities.”

But the U.S. Environmental Protection Agency, which declared in a 2004 study (pdf) that fracking posed “little or no threat to underground sources of drinking water,” is now reconsidering its conclusion. The state of New York has stopped issuing horizontal drilling permits for the Marcellus Shale while it completes an environmental review. The Marcellus sits atop the Delaware River watershed, which supplies drinking water to 17 million people, including residents of Philadelphia and New York City. A bill now under consideration on Capitol Hill would grant the EPA oversight of fracking and force drilling companies, which are currently exempt from portions of the Clean Water Act, to disclose the chemicals they use in fracturing fluids.

At every checkpoint in the development pipeline, Ingraffea says, there is potential for trouble. “It’s disturbing how densely they’re trying to pack these wells. The record I know of is 16 wells on one pad. The enormous amount of water injected into such a small volume of rock is creating much more pressure than there has ever been there.” There have been reports of small earthquakes near some injection sites for fracking waste in Texas, a state not known for seismic activity. Last fall a swarm of about 500 mini-quakes rocked central Arkansas near the Fayetteville Shale, and a 4.7-magnitude earthquake in February prompted the Arkansas Oil and Gas Commission to order two drilling companies to temporarily suspend operations.

Add a host of unknowns—like possible faulty cement jobs in the pipes, which was the cause of the Deepwater Horizon blowout in the Gulf of Mexico, or hitting an abandoned gas and oil well—and the potential for danger expands exponentially.

But it is the threat to the water supply that prompts the loudest warnings. A team of environmental scientists hired by New York City in 2009 to evaluate fracking’s environmental impact concluded that the process could be “catastrophic” to the city’s water supply because it degraded water quality and exposed residents to potentially “chronic low levels of toxic chemicals.”

Health risks aside, natural gas may ultimately prove no cleaner than America’s other abundant domestic fossil fuel, coal. Cornell University researchers factored in the carbon emissions over the course of natural gas’s life cycle when it is extracted using hydraulic fracturing—which includes drilling the wells, erecting the construction sites, building pipelines to transport the gas, fueling the pumps that force the water underground, and transporting the wastewater—and concluded that natural gas is dirtier than coal. Another wild card is methane, which inevitably seeps out during the extraction process, escaping from imperfect joints on thousands of pipes, valves, compressors, and holding tanks, or simply migrating through hairline cracks in the rock. Methane is 20 times as damaging a greenhouse gas as carbon dioxide.

The solution to all of these concerns may be to make fracking more efficient and less toxic. One promising way to do that was recently tested on a string of more than a dozen natural gas wells in the heart of the Texas oil fields. Instead of pumping millions of gallons of water and fracturing fluid into the earth, the company GasFrac used a liquefied petroleum gas gel—propane gas compressed into a thick fluid—to break up the rock. This simple switch could pave the way toward a more environmentally friendly method of extracting natural gas that would do less collateral damage to the land and water while dramatically reducing fracking’s carbon footprint at the same time.

Liquefied petroleum gas (LPG) has a number of advantages over the chemical-laced water typically used as a fracking fluid. Although it is pumped into the well as a gelled liquid, it converts back into gas while underground. It can then be sucked back out as the natural gas is extracted from the reservoir, meaning that there is a virtually complete recovery of the fracking fluid; water-based methods have roughly a 50 percent recovery rate. Since the LPG is almost 100 percent retrievable, the time and effort of recovering, filtering, and reusing the fluid are dramatically reduced. Propane is less dense than water, so LPG-based fracking projects should require less truck traffic and smaller staging areas, which cuts carbon emissions. This approach also eliminates the need for freshwater tanks or pits for waste and bypasses many of the concerns about tainting groundwater.

Without switching to LPG fracking, some companies are already attempting to clean up natural gas drilling to address the concerns of local communities. In western Colorado, for example, Antero Resources Corp. negotiated an agreement with civic leaders to use nontoxic hydraulic fracturing fluids, monitor water supplies, and avoid the use of wastewater disposal pits. To encourage better drilling practices, the Houston Advanced Research Center—a consortium supported by government, foundations, and private industry—launched the Environmentally Friendly Drilling Scorecard at the end of last year. The scorecard awards companies up to five stars based on their use of cleaner oil and gas drilling techniques, including smaller and more lightweight rigs, well site and road construction that employs low-impact technologies, lower-emission power packages, or advanced water-management systems.

The scorecard is still in the test phase, so no companies drilling in the Marcellus Shale have yet publicly adopted it, though Halliburton has agreed to disclose the chemicals it is using in its fracking fluids. Ratcheting up the pressure, the EPA and the Pennsylvania Department of Environmental Protection are both taking a closer look at the environmental costs of fracking and are investigating the uranium findings made by Tracy Bank, who continues to research how fracking impacts toxic metals. The EPA is also aggressively prodding state regulators and others involved in natural gas extraction in the Marcellus Shale to release what they know about radioactivity in the wastewater.

Even skeptics like the NRDC’s Kate Sinding recognize that fracking is not going away. The economic and environmental factors in favor of natural gas are simply too powerful. “Nothing is ever going to be completely safe or perfect,” Sinding says. “The key is to get an inventory of best practices and then make sure you have the resources to implement and enforce them.” As the Deepwater Horizon oil spill proved, allowing drilling technology to outpace the development of sound safeguards is courting disaster. Especially when that drilling is going on in someone’s backyard.